Advances in tepary bean (Phaseolus acutifolius A. Gray) genetics and breeding

Transcription

1 Advances in tepary bean (Phaseolus acutifolius A. Gray) genetics and breeding Tim Porch, Iveth Rodriguez, John Hart, Anna Vargas, Juan Carlos Rosas, Mark Brick, James Beaver Feed the Future Innovation Lab for Collaborative Research on Grain Legumes

2 Overview Background on tepary beans Advances in genetics and breeding of traits limiting expansion of tepary production BCMV BGYMV Common bacterial blight Web blight Agronomic/seed characteristics

3 Tepary beans likely originated from the Sonoran desert -Naturally adapted to heat and drought stress Sister species of common bean Similar nutritional and agronomic characteristics Sonoran desert From Wikipedia.com

4 Traditional system of tepary production Art by Leonard Chana in Desert Plants (1983) Tepary field, Coolidge, Arizona, 1983 Burgess, 1983

5 Problem: Predicted 60% reduction in bean area in Sub-Saharan Africa for 2100 due to climate change (Rippke et al., 2016) Extent of transformation (%) Extent of transformation (%) Grain legumes (RCP6.0) 40 Bean 35 Groundnut Year Grain legumes (RCP8.5) Bean Groundnut Year

6 Yield, kg/ha Tepary part of the solution? Heat trial, Juana Diaz, Puerto Rico in 2015 (33⁰C/ 24⁰C) 500 kg/ha Andean (250) Mean= 83 kg/ha Meso (120) Mean= 403 kg/ha Tepary (160) Mean= 1,627 kg/ha

7 Tepary diversity G40078 Wild tenuifolius Texas G40097 Wild acutifolius Durango PI Landrace Arizona (Hopi) G40018 Landrace Chiapas

8 John Hart Tepary Diversity Panel (TDP) Germplasm 314 Accessions assembled, increased, & genotyped (158 wild, 156 cultivated) CIAT (mostly), USDA-GRIN, USDA-TARS Tested extensively in field trials (cultivated types) Used for study of BCMV, BGYMV, Agronomic traits Genotyping ApeKI genotyping-by-sequencing (GBS) 384-plex library 4 lanes, single end sequencing on Illumina 2500 SNP calling & filtering with TASSEL using P. vulgaris genome 20,364 SNPs (maf=0.05) in 80% of all accessions - 7,642 SNPs in cultivated germplasm - 23,070 SNPs in wild germplasm

9 faststructure - 20,364 SNPs (SCov=0.80, maf=0.05); K = 8

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12 Key tepary production constraints Key disease constraints for production zones Bean Common Mosaic Virus (BCMV); BCMNV Bean Golden Yellow Mosaic Virus (BGYMV) Bacterial blight (X. axonopodis) Web blight (R. solani) Agronomic and seed traits Common bean Tepary

13 Bean Common Mosaic Virus (BCMV) CULTIVATED WILD Veinal Necrosis PL No Symptoms Veinal Necrosis No Symptoms Mosaic Leaf Curl Mosaic Necrotic Local Lesions No Symptoms Necrotic Local Lesions No Symptoms

14 J. Hart & A. Vargas Identification of resistance to BCMNV NL3 2 Genes identified with GWAS in TDP Scored ELISA readings Resistance to NL 3 D in 11 resistant wild accessions out of 149 wild accessions (maf = 0.074)

15 Geographical distribution of resistance to BCMNV NL3 Sonoran Desert Durango Central Plateau West of Sierra Madre

16 Bean Golden Yellow Mosaic Virus (BGYMV) Zamorano, Honduras 1/2017

17 Iveth Rodriguez Common bacterial blight Source of resistance VAX lines (Singh y Muñoz, 1999) Feed the Future Innovation Lab for Collaborative Fuente Research de Resistencia on Grain Líneas Legumes VAX (Singh y Muñoz, 1999)

18 142, F5:8 RILs RIL Population G40001/G40022 ApeKI genotyping-by-sequencing (GBS) 1,343 SNPs mapped using P. vulgaris reference genome QTLs analysis: WinQTLCartographer, CIM, LOD set with permutation analysis G40001 G40022 Genome Sequence: (Buell, MSU; McClean, NDSU, Schmutz, Hudson Alpha) 12.3 g 15.3 g

19 LOD LOD LOD Chromosome Posición (cm) Initial QTL analysis of bacterial blight - Greenhouse Trial - X.a. strain Chromosome Posición (cm) Source of resistance: G40001 Chromosome 10B Posición (cm)

20 LOD LOD LOD Chromosome Posición (cm) Initial QTL analysis of web blight Field trial, Isabela Chromosome Posición (cm) Source of resistance: G Chromosome 10A Feed the Posición Future (cm) Innovation Lab for Collaborative Research on Grain Legumes

21 Key Agronomic Traits Seed characteristics Seed nutritional quality Cooking time Seed color, shape, and size

22 Nutrition: Tepary similar to common bean Genotype Tepary bean Proximate analysis Prote in Fat Fiber Ash Fructo se Gluco se Sugar analysis Malto se Sucro se Raffino se Stachyo se Verbasc ose Tep Tep Neb-T-1s Tep Tep Tep Mean Common bean TARS-MST Verano Zorro Mean (Porch et al., 2016) (Porch et. al 2016)

23 Tepary nutritional and cooking characteristics Collaboration: K. Cichy (ARS) Mike Grusak (ARS) Porch et. al 2016 Collaboration with K. Cichy

24 Expansion of seed classes

25 Expansion of seed classes

26 Evaluation of seed shape and size Smart grain

27 LOD LOD LOD Chromosome Posición (cm) QTL for Seed area SmartGrain Chromosome Posición (cm) Chr. 7 in tepary Seed perimeter Seed width Seed length Seed circularity Chromosome Posición (cm)

28 LOD QTL analysis of seed color in RIL population (Hue, L) -Overlapping intervals of color and seed size QTL 5 Chromosome Posición (cm) Coincides with location of P gene in common bean -P. McClean, K. Bett

29 5.00 Principal component analysis -RIL population 2.50 DMF DF Biomasa CP 2 (14.3%) 0.00 G40001 Hue L Temp35 Vigor. Temp42 Circularidad Croma PCS ICV IC Width Area Length Perimeter Ancho Area Largo Perimetro G Association of seed size and colored seed CP 1 (28.6%)

30 First QTL identified common bean seed size associated with seed color (Sax, 1923)

31 GWAS of Tepary Diversity Panel (TDP) under heat Juana Diaz, PR 2015 (148 entries, 18,500 SNPs) Yield kg/ha Harvest index Chromosome

32 LOD 4 3 Chromosome 3 Initial QTLs identified under heat in RIL pop. Juana Diaz, PR Posición (cm) Chromosome 3 Yield under heat -from G Pollen shed under heat -from G

33 Breeding: Tepary Adapatiation Trials (TAT) Methods: RCBD lines Local check Feed the Feed Future theinnovation Future countries Lab for Collaborative in green Research on Grain Legumes

34 Zanzíbar, Tanzania 2015 (Susan Nchimbi) Zamorano, Honduras 2014 (Juan Carlos Rosas)

35 CIAT, Malawi 2017 (Rowland Chirwa) Ft. Collins, Colorado 2016 (Mark Brick)

36 Haiti, 2017 (Raphael Colbert, Emmanuel Prophete) Isabela, Puerto Rico 2016

37 (kg/ha) First release of improved tepary bean, 2013 Juana Diaz, PR 2011 Tepary Neb-T-1-s 30 PI PI PI s 13 PI TB Verano Reduced Stress (kg/ha) Bean Release of germplasm TARS-Tep 22 (off-white) TARS-Tep 32 (yellow) (Porch et al., 2013)

38 Results of TAT Trials Burkina Faso, Yield, kg/ha, 2015 Pods/ Seeds/ Genotype Germ. DTF DTM SPAD Plts Plt pod HSW Yield Biomass Virus days days # # # grams kg/ha TM/ha Check Tep Tep Tep Tep Tep Tep Tep Tep Mean LSD NS 1.3 NS NS CV Release considered in B. Faso by Issa Drabo (from Thesis: Topan, 2016)

39 Yield under high temperature in Puerto Rico in 2015 Yield, kg/ha 33⁰C/ 24⁰C 500 kg/ha Andean (250) Meso (120) Tepary (160) Mean= Mean= Mean= Single plant selection for plants showing tolerance to BGYMV 83 kg/ha 403 kg/ha 1,627 kg/ha Feed the Future Innovation Lab for Collaborative Research on Grain Legumes Zamorano, Honduras 1/2017 (Juan Carlos Rosas)

40 Collaborators USDA-ARS Karen Cichy Mike Grusak TARS Bean Team: John Hart, Iveth Rodriguez, Ana Varga, Stephanie Cosme CIAT Germplasm Repository Colorado State University Mark Brick INERA Issa Drabo Sokoine University Susan Nchimbi University of Puerto Rico Jim Beaver Zamorano Juan Carlos Rosas